The point is that a virus is a brute-force mechanism. This introduces a probability (even a low one) that a virus might "choose" to become more nasty in order to elicit a response from a "vaccinated" population.

Vaccinated is in quotes because many of the current vaccines are, admittedly, therapeutics rather than vaccines. The classical definition of a vaccine is something that prevents infection entirely. The current politicized definition of vaccine is something that decreases mortality / symptoms for a specific disease.

We know that these vaccines are "leaky", and now it's just up to random chance to determine whether or not this will lead to a scenario like the chickens. I believe the chance is very low, but it's there.